The resulting optimization problem is convex and amenable, thanks to smoothing theory, to state-of-the-art optimization techniques that leverage the sparsity of the solutions.

Trajectory inference seeks to recover the temporal dynamics of a population from snapshots of its (uncoupled) temporal marginals, i.e. where observed particles are not tracked over time. Lavenant et al. arXiv:2102.09204 addressed this challenging problem under a stochastic differential equation (SDE) model with a gradient-driven drift in the observed space, introducing a minimum entropy estimator relative to the Wiener measure. Chizat et al. arXiv:2205.07146 then provided a practical grid-free mean-field Langevin (MFL) algorithm using Schr\"odinger bridges. Motivated by the overwhelming success of observable state space models in the traditional paired trajectory inference problem (e.g. target tracking), we extend the above framework to a class of latent SDEs in the form of observable state space models. In this setting, we use partial observations to infer trajectories in the latent space under a specified dynamics model (e.g. the constant velocity/acceleration models from target tracking). We introduce PO-MFL to solve this latent trajectory inference problem and provide theoretical guarantees by extending the results of arXiv:2102.09204 to the partially observed setting. We leverage the MFL framework of arXiv:2205.07146, yielding an algorithm based on entropic OT between dynamics-adjusted adjacent time marginals. Experiments validate the robustness of our method and the exponential convergence of the MFL dynamics, and demonstrate significant outperformance over the latent-free method of arXiv:2205.07146 in key scenarios.

We devise a theoretical framework and a numerical method to infer trajectories of a stochastic process from snapshots of its temporal marginals. This problem arises in the analysis of single cell RNA-sequencing data, which provide high dimensional measurements of cell states but cannot track the trajectories of the cells over time. We prove that for a class of stochastic processes it is possible to recover the ground truth trajectories from limited samples of the temporal marginals at each time-point, and provide an efficient algorithm to do so in practice. The method we develop, Global Waddington-OT (gWOT), boils down to a smooth convex optimization problem posed globally over all time-points involving entropy-regularized optimal transport. We demonstrate that this problem can be solved efficiently in practice and yields good reconstructions, as we show on several synthetic and real datasets.